mirror of
https://github.com/nqrduck/quackseq.git
synced 2024-11-09 21:10:01 +00:00
Moved simlator to own repository.
This commit is contained in:
jupfi
parent
e504f0154d
commit
a265cb7d65
4 changed files with 0 additions and 776 deletions
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@ -1,17 +0,0 @@
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from quackseq.spectrometer.spectrometer import Spectrometer
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from .simulator_model import SimulatorModel
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from .simulator_controller import SimulatorController
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class Simulator(Spectrometer):
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def __init__(self):
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self.model = SimulatorModel()
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self.controller = SimulatorController(self.model)
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def run_sequence(self, sequence):
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result =self.controller.run_sequence(sequence)
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return result
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def set_averages(self, value: int):
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self.model.average = value
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"""The controller module for the simulator spectrometer."""
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import logging
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from datetime import datetime
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import numpy as np
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from quackseq.spectrometer.spectrometer_controller import SpectrometerController
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from quackseq.measurement import Measurement
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from quackseq.pulseparameters import TXPulse, RXReadout
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from quackseq.pulsesequence import QuackSequence
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from nqr_blochsimulator.classes.pulse import PulseArray
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from nqr_blochsimulator.classes.sample import Sample
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from nqr_blochsimulator.classes.simulation import Simulation
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logger = logging.getLogger(__name__)
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class SimulatorController(SpectrometerController):
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"""The controller class for the nqrduck simulator module."""
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def __init__(self, model):
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"""Initializes the SimulatorController."""
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super().__init__()
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self.model = model
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def run_sequence(self, sequence: QuackSequence) -> None:
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"""This method is called when the start_measurement signal is received from the core.
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It will becalled if the simulator is the active spectrometer.
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This will start the simulation based on the settings and the pulse sequence.
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"""
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logger.debug("Starting simulation")
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sample = self.get_sample_from_settings()
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logger.debug("Sample: %s", sample.name)
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dwell_time = self.calculate_dwelltime(sequence)
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logger.debug("Dwell time: %s", dwell_time)
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try:
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pulse_array = self.translate_pulse_sequence(sequence, dwell_time)
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except AttributeError:
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logger.warning("Could not translate pulse sequence")
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return
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simulation = self.get_simulation(sample, pulse_array)
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result = simulation.simulate()
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tdx = (
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np.linspace(0, float(self.calculate_simulation_length(sequence)), len(result)) * 1e6
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)
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rx_begin, rx_stop = self.translate_rx_event(sequence)
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# If we have a RX event, we need to cut the result to the RX event
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if rx_begin and rx_stop:
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evidx = np.where((tdx > rx_begin) & (tdx < rx_stop))[0]
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tdx = tdx[evidx]
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result = result[evidx]
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# Measurement name date + module + target frequency + averages + sequence name
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name = f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')} - Simulator - {self.model.target_frequency / 1e6} MHz - {self.model.averages} averages - {sequence.name}"
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logger.debug(f"Measurement name: {name}")
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measurement_data = Measurement(
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name,
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tdx,
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result / simulation.averages,
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sample.resonant_frequency,
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# frequency_shift=self.module.model.if_frequency,
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)
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return measurement_data
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def get_sample_from_settings(self) -> Sample:
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"""This method creates a sample object based on the settings in the model.
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Returns:
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Sample: The sample object created from the settings.
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"""
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model = self.model
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atom_density = None
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sample_volume = None
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sample_length = None
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sample_diameter = None
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for samplesetting in model.settings[self.model.SAMPLE]:
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logger.debug("Sample setting: %s", samplesetting.name)
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if samplesetting.name == model.NAME:
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name = samplesetting.value
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elif samplesetting.name == model.DENSITY:
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density = float(samplesetting.value)
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elif samplesetting.name == model.MOLAR_MASS:
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molar_mass = float(samplesetting.value)
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elif samplesetting.name == model.RESONANT_FREQUENCY:
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resonant_frequency = float(samplesetting.value)
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elif samplesetting.name == model.GAMMA:
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gamma = float(samplesetting.value)
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elif samplesetting.name == model.NUCLEAR_SPIN:
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nuclear_spin = float(samplesetting.value)
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elif samplesetting.name == model.SPIN_FACTOR:
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spin_factor = float(samplesetting.value)
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elif samplesetting.name == model.POWDER_FACTOR:
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powder_factor = float(samplesetting.value)
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elif samplesetting.name == model.FILLING_FACTOR:
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filling_factor = float(samplesetting.value)
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elif samplesetting.name == model.T1:
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T1 = float(samplesetting.value)
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elif samplesetting.name == model.T2:
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T2 = float(samplesetting.value)
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elif samplesetting.name == model.T2_STAR:
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T2_star = float(samplesetting.value)
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elif samplesetting.name == model.ATOM_DENSITY:
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atom_density = float(samplesetting.value)
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elif samplesetting.name == model.SAMPLE_VOLUME:
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sample_volume = float(samplesetting.value)
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elif samplesetting.name == model.SAMPLE_LENGTH:
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sample_length = float(samplesetting.value)
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elif samplesetting.name == model.SAMPLE_DIAMETER:
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sample_diameter = float(samplesetting.value)
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else:
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logger.warning("Unknown sample setting: %s", samplesetting.name)
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self.module.nqrduck_signal.emit(
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"notification",
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["Error", "Unknown sample setting: " + samplesetting.name],
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)
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return None
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sample = Sample(
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name=name,
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density=density,
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molar_mass=molar_mass,
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resonant_frequency=resonant_frequency,
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gamma=gamma,
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nuclear_spin=nuclear_spin,
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spin_factor=spin_factor,
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powder_factor=powder_factor,
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filling_factor=filling_factor,
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T1=T1,
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T2=T2,
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T2_star=T2_star,
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atom_density=atom_density,
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sample_volume=sample_volume,
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sample_length=sample_length,
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sample_diameter=sample_diameter,
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)
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return sample
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def translate_pulse_sequence(self, sequence : QuackSequence, dwell_time: float) -> PulseArray:
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"""This method translates the pulse sequence from the core to a PulseArray object needed for the simulation.
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Args:
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sequence (QuackSequence): The pulse sequence from the core.
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dwell_time (float): The dwell time in seconds.
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Returns:
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PulseArray: The pulse sequence translated to a PulseArray object.
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"""
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events = sequence.events
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amplitude_array = list()
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for event in events:
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logger.debug("Event %s has parameters: %s", event.name, event.parameters)
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for parameter in event.parameters.values():
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logger.debug(
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"Parameter %s has options: %s", parameter.name, parameter.options
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)
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if (
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parameter.name == sequence.TX_PULSE
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and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value
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> 0
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):
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logger.debug(f"Adding pulse: {event.duration} s")
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# If we have a pulse, we need to add it to the pulse array
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pulse_shape = parameter.get_option_by_name(
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TXPulse.TX_PULSE_SHAPE
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).value
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pulse_amplitude = abs(
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pulse_shape.get_pulse_amplitude(
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event.duration, resolution=dwell_time
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)
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)
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amplitude_array.append(pulse_amplitude)
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elif (
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parameter.name == sequence.TX_PULSE
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and parameter.get_option_by_name(TXPulse.RELATIVE_AMPLITUDE).value
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== 0
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):
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# If we have a wait, we need to add it to the pulse array
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amplitude_array.append(np.zeros(int(event.duration / dwell_time)))
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amplitude_array = np.concatenate(amplitude_array)
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# This has not yet been implemented right now the phase is always 0
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phase_array = np.zeros(len(amplitude_array))
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pulse_array = PulseArray(
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pulseamplitude=amplitude_array,
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pulsephase=phase_array,
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dwell_time=float(dwell_time),
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)
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return pulse_array
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def get_simulation(self, sample: Sample, pulse_array: PulseArray) -> Simulation:
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"""This method creates a simulation object based on the settings and the pulse sequence.
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Args:
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sample (Sample): The sample object created from the settings.
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pulse_array (PulseArray): The pulse sequence translated to a PulseArray object.
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Returns:
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Simulation: The simulation object created from the settings and the pulse sequence.
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"""
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model = self.model
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# noise = float(model.get_setting_by_name(model.NOISE).value)
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simulation = Simulation(
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sample=sample,
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pulse=pulse_array,
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number_isochromats=int(
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model.get_setting_by_name(model.NUMBER_ISOCHROMATS).value
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),
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initial_magnetization=float(
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model.get_setting_by_name(model.INITIAL_MAGNETIZATION).value
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),
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gradient=float(model.get_setting_by_name(model.GRADIENT).value),
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noise=float(model.get_setting_by_name(model.NOISE).value),
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length_coil=float(model.get_setting_by_name(model.LENGTH_COIL).value),
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diameter_coil=float(model.get_setting_by_name(model.DIAMETER_COIL).value),
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number_turns=float(model.get_setting_by_name(model.NUMBER_TURNS).value),
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q_factor_transmit=float(
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model.get_setting_by_name(model.Q_FACTOR_TRANSMIT).value
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),
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q_factor_receive=float(
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model.get_setting_by_name(model.Q_FACTOR_RECEIVE).value
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),
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power_amplifier_power=float(
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model.get_setting_by_name(model.POWER_AMPLIFIER_POWER).value
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),
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gain=float(model.get_setting_by_name(model.GAIN).value),
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temperature=float(model.get_setting_by_name(model.TEMPERATURE).value),
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averages=int(model.averages),
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loss_TX=float(model.get_setting_by_name(model.LOSS_TX).value),
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loss_RX=float(model.get_setting_by_name(model.LOSS_RX).value),
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conversion_factor=float(
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model.get_setting_by_name(model.CONVERSION_FACTOR).value
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),
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)
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return simulation
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def calculate_dwelltime(self, sequence : QuackSequence) -> float:
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"""This method calculates the dwell time based on the settings and the pulse sequence.
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Returns:
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float: The dwell time in seconds.
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"""
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n_points = int(
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self.model.get_setting_by_name(self.model.NUMBER_POINTS).value
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)
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simulation_length = self.calculate_simulation_length(sequence)
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dwell_time = simulation_length / n_points
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return dwell_time
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def calculate_simulation_length(self, sequence : QuackSequence) -> float:
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"""This method calculates the simulation length based on the settings and the pulse sequence.
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Returns:
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float: The simulation length in seconds.
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"""
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events = sequence.events
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simulation_length = 0
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for event in events:
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simulation_length += event.duration
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return simulation_length
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def translate_rx_event(self, sequence : QuackSequence) -> tuple:
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"""This method translates the RX event of the pulse sequence to the limr object.
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Returns:
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tuple: A tuple containing the start and stop time of the RX event in µs
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"""
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# This is a correction factor for the RX event. The offset of the first pulse is 2.2µs longer than from the specified samples.
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events = sequence.events
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previous_events_duration = 0
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# offset = 0
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rx_duration = 0
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for event in events:
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logger.debug("Event %s has parameters: %s", event.name, event.parameters)
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for parameter in event.parameters.values():
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logger.debug(
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"Parameter %s has options: %s", parameter.name, parameter.options
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)
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if (
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parameter.name == sequence.RX_READOUT
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and parameter.get_option_by_name(RXReadout.RX).value
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):
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# Get the length of all previous events
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previous_events = events[: events.index(event)]
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previous_events_duration = sum(
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[event.duration for event in previous_events]
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)
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rx_duration = event.duration
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rx_begin = float(previous_events_duration)
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if rx_duration:
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rx_stop = rx_begin + float(rx_duration)
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return rx_begin * 1e6, rx_stop * 1e6
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else:
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return None, None
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def set_frequency(self, value: str) -> None:
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"""This method is called when the set_frequency signal is received from the core.
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For the simulator this just prints a warning that the simulator is selected.
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Args:
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value (str) : The new frequency in MHz.
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"""
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logger.debug("Setting frequency to: %s", value)
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try:
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self.module.model.target_frequency = float(value)
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logger.debug("Successfully set frequency to: %s", value)
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except ValueError:
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logger.warning("Could not set frequency to: %s", value)
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self.module.nqrduck_signal.emit(
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"notification", ["Error", "Could not set frequency to: " + value]
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)
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self.module.nqrduck_signal.emit("failure_set_frequency", value)
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def set_averages(self, value: str) -> None:
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"""This method is called when the set_averages signal is received from the core.
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It sets the averages in the model used for the simulation.
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Args:
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value (str): The value to set the averages to.
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"""
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logger.debug("Setting averages to: %s", value)
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try:
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self.module.model.averages = int(value)
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logger.debug("Successfully set averages to: %s", value)
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except ValueError:
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logger.warning("Could not set averages to: %s", value)
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self.module.nqrduck_signal.emit(
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"notification", ["Error", "Could not set averages to: " + value]
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)
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self.module.nqrduck_signal.emit("failure_set_averages", value)
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|
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@ -1,327 +0,0 @@
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"""The model module for the simulator spectrometer."""
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|
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import logging
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|
||||||
from quackseq.spectrometer.spectrometer_model import SpectrometerModel
|
|
||||||
from quackseq.spectrometer.spectrometer_settings import IntSetting, FloatSetting, StringSetting
|
|
||||||
from quackseq.pulseparameters import TXPulse, RXReadout
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class SimulatorModel(SpectrometerModel):
|
|
||||||
"""Model class for the simulator spectrometer."""
|
|
||||||
|
|
||||||
# Simulation settings
|
|
||||||
NUMBER_POINTS = "N. simulation points"
|
|
||||||
NUMBER_ISOCHROMATS = "N. of isochromats"
|
|
||||||
INITIAL_MAGNETIZATION = "Initial magnetization"
|
|
||||||
GRADIENT = "Gradient (mT/m))"
|
|
||||||
NOISE = "Noise (uV)"
|
|
||||||
|
|
||||||
# Hardware settings
|
|
||||||
LENGTH_COIL = "Length coil (m)"
|
|
||||||
DIAMETER_COIL = "Diameter coil (m)"
|
|
||||||
NUMBER_TURNS = "Number turns"
|
|
||||||
Q_FACTOR_TRANSMIT = "Q factor Transmit"
|
|
||||||
Q_FACTOR_RECEIVE = "Q factor Receive"
|
|
||||||
POWER_AMPLIFIER_POWER = "PA power (W)"
|
|
||||||
GAIN = "Gain"
|
|
||||||
TEMPERATURE = "Temperature (K)"
|
|
||||||
AVERAGES = "Averages"
|
|
||||||
LOSS_TX = "Loss TX (dB)"
|
|
||||||
LOSS_RX = "Loss RX (dB)"
|
|
||||||
CONVERSION_FACTOR = "Conversion factor"
|
|
||||||
|
|
||||||
# Sample settings, this will be done in a separate module later on
|
|
||||||
NAME = "Name"
|
|
||||||
DENSITY = "Density (g/cm^3)"
|
|
||||||
MOLAR_MASS = "Molar mass (g/mol)"
|
|
||||||
RESONANT_FREQUENCY = "Resonant freq. (Hz)"
|
|
||||||
GAMMA = "Gamma (Hz/T)"
|
|
||||||
NUCLEAR_SPIN = "Nuclear spin"
|
|
||||||
SPIN_FACTOR = "Spin factor"
|
|
||||||
POWDER_FACTOR = "Powder factor"
|
|
||||||
FILLING_FACTOR = "Filling factor"
|
|
||||||
T1 = "T1 (s)"
|
|
||||||
T2 = "T2 (s)"
|
|
||||||
T2_STAR = "T2* (s)"
|
|
||||||
ATOM_DENSITY = "Atom density (1/cm^3)"
|
|
||||||
SAMPLE_VOLUME = "Sample volume (m^3)"
|
|
||||||
SAMPLE_LENGTH = "Sample length (m)"
|
|
||||||
SAMPLE_DIAMETER = "Sample diameter (m)"
|
|
||||||
|
|
||||||
# Categories of the settings
|
|
||||||
SIMULATION = "Simulation"
|
|
||||||
HARDWARE = "Hardware"
|
|
||||||
EXPERIMENTAL_Setup = "Experimental Setup"
|
|
||||||
SAMPLE = "Sample"
|
|
||||||
|
|
||||||
def __init__(self):
|
|
||||||
"""Initializes the SimulatorModel."""
|
|
||||||
super().__init__()
|
|
||||||
|
|
||||||
# Simulation settings
|
|
||||||
number_of_points_setting = IntSetting(
|
|
||||||
self.NUMBER_POINTS,
|
|
||||||
8192,
|
|
||||||
"Number of points used for the simulation. This influences the dwell time in combination with the total event simulation given by the pulse sequence.",
|
|
||||||
min_value=0,
|
|
||||||
)
|
|
||||||
self.add_setting(
|
|
||||||
number_of_points_setting,
|
|
||||||
self.SIMULATION,
|
|
||||||
)
|
|
||||||
|
|
||||||
number_of_isochromats_setting = IntSetting(
|
|
||||||
self.NUMBER_ISOCHROMATS,
|
|
||||||
1000,
|
|
||||||
"Number of isochromats used for the simulation. This influences the computation time.",
|
|
||||||
min_value=0,
|
|
||||||
max_value=10000,
|
|
||||||
)
|
|
||||||
self.add_setting(number_of_isochromats_setting, self.SIMULATION)
|
|
||||||
|
|
||||||
initial_magnetization_setting = FloatSetting(
|
|
||||||
self.INITIAL_MAGNETIZATION,
|
|
||||||
1,
|
|
||||||
"Initial magnetization",
|
|
||||||
min_value=0,
|
|
||||||
)
|
|
||||||
self.add_setting(initial_magnetization_setting, self.SIMULATION)
|
|
||||||
|
|
||||||
# This doesn't really do anything yet
|
|
||||||
gradient_setting = FloatSetting(
|
|
||||||
self.GRADIENT,
|
|
||||||
1,
|
|
||||||
"Gradient",
|
|
||||||
)
|
|
||||||
self.add_setting(gradient_setting, self.SIMULATION)
|
|
||||||
|
|
||||||
noise_setting = FloatSetting(
|
|
||||||
self.NOISE,
|
|
||||||
2,
|
|
||||||
"Adds a specified level of random noise to the simulation to mimic real-world signal variations.",
|
|
||||||
min_value=0,
|
|
||||||
max_value=100,
|
|
||||||
)
|
|
||||||
self.add_setting(noise_setting, self.SIMULATION)
|
|
||||||
|
|
||||||
# Hardware settings
|
|
||||||
coil_length_setting = FloatSetting(
|
|
||||||
self.LENGTH_COIL,
|
|
||||||
30e-3,
|
|
||||||
"The length of the sample coil within the hardware setup.",
|
|
||||||
min_value=1e-3,
|
|
||||||
)
|
|
||||||
self.add_setting(coil_length_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
coil_diameter_setting = FloatSetting(
|
|
||||||
self.DIAMETER_COIL,
|
|
||||||
8e-3,
|
|
||||||
"The diameter of the sample coil.",
|
|
||||||
min_value=1e-3,
|
|
||||||
)
|
|
||||||
self.add_setting(coil_diameter_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
number_turns_setting = FloatSetting(
|
|
||||||
self.NUMBER_TURNS,
|
|
||||||
8,
|
|
||||||
"The total number of turns of the sample coil.",
|
|
||||||
min_value=1,
|
|
||||||
)
|
|
||||||
self.add_setting(number_turns_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
q_factor_transmit_setting = FloatSetting(
|
|
||||||
self.Q_FACTOR_TRANSMIT,
|
|
||||||
80,
|
|
||||||
"The quality factor of the transmit path, which has an effect on the field strength for excitation.",
|
|
||||||
min_value=1,
|
|
||||||
)
|
|
||||||
self.add_setting(q_factor_transmit_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
q_factor_receive_setting = FloatSetting(
|
|
||||||
self.Q_FACTOR_RECEIVE,
|
|
||||||
80,
|
|
||||||
"The quality factor of the receive path, which has an effect on the final SNR.",
|
|
||||||
min_value=1,
|
|
||||||
)
|
|
||||||
self.add_setting(q_factor_receive_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
power_amplifier_power_setting = FloatSetting(
|
|
||||||
self.POWER_AMPLIFIER_POWER,
|
|
||||||
110,
|
|
||||||
"The power output capability of the power amplifier, determines the strength of pulses that can be generated.",
|
|
||||||
min_value=0.1,
|
|
||||||
)
|
|
||||||
self.add_setting(power_amplifier_power_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
gain_setting = FloatSetting(
|
|
||||||
self.GAIN,
|
|
||||||
6000,
|
|
||||||
"The amplification factor of the receiver chain, impacting the final measured signal amplitude.",
|
|
||||||
min_value=0.1,
|
|
||||||
)
|
|
||||||
self.add_setting(gain_setting, self.HARDWARE)
|
|
||||||
|
|
||||||
temperature_setting = FloatSetting(
|
|
||||||
self.TEMPERATURE,
|
|
||||||
300,
|
|
||||||
"The absolute temperature during the experiment. This influences the SNR of the measurement.",
|
|
||||||
min_value=0.1,
|
|
||||||
max_value=400,
|
|
||||||
)
|
|
||||||
self.add_setting(temperature_setting, self.EXPERIMENTAL_Setup)
|
|
||||||
|
|
||||||
loss_tx_setting = FloatSetting(
|
|
||||||
self.LOSS_TX,
|
|
||||||
25,
|
|
||||||
"The signal loss occurring in the transmission path, affecting the effective RF pulse power.",
|
|
||||||
min_value=0.1,
|
|
||||||
max_value=60,
|
|
||||||
)
|
|
||||||
self.add_setting(loss_tx_setting, self.EXPERIMENTAL_Setup)
|
|
||||||
|
|
||||||
loss_rx_setting = FloatSetting(
|
|
||||||
self.LOSS_RX,
|
|
||||||
25,
|
|
||||||
"The signal loss in the reception path, which can reduce the signal that is ultimately detected.",
|
|
||||||
min_value=0.1,
|
|
||||||
max_value=60,
|
|
||||||
)
|
|
||||||
self.add_setting(loss_rx_setting, self.EXPERIMENTAL_Setup)
|
|
||||||
|
|
||||||
conversion_factor_setting = FloatSetting(
|
|
||||||
self.CONVERSION_FACTOR,
|
|
||||||
2884,
|
|
||||||
"Conversion factor (spectrometer units / V)",
|
|
||||||
)
|
|
||||||
self.add_setting(
|
|
||||||
conversion_factor_setting,
|
|
||||||
self.EXPERIMENTAL_Setup,
|
|
||||||
) # Conversion factor for the LimeSDR based spectrometer
|
|
||||||
|
|
||||||
# Sample settings
|
|
||||||
sample_name_setting = StringSetting(
|
|
||||||
self.NAME,
|
|
||||||
"BiPh3",
|
|
||||||
"The name of the sample.",
|
|
||||||
)
|
|
||||||
self.add_setting(sample_name_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
density_setting = FloatSetting(
|
|
||||||
self.DENSITY,
|
|
||||||
1.585e6,
|
|
||||||
"The density of the sample. This is used to calculate the number of spins in the sample volume.",
|
|
||||||
min_value=0.1,
|
|
||||||
)
|
|
||||||
self.add_setting(density_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
molar_mass_setting = FloatSetting(
|
|
||||||
self.MOLAR_MASS,
|
|
||||||
440.3,
|
|
||||||
"The molar mass of the sample. This is used to calculate the number of spins in the sample volume.",
|
|
||||||
min_value=0.1,
|
|
||||||
)
|
|
||||||
self.add_setting(molar_mass_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
resonant_frequency_setting = FloatSetting(
|
|
||||||
self.RESONANT_FREQUENCY,
|
|
||||||
83.56e6,
|
|
||||||
"The resonant frequency of the observed transition.",
|
|
||||||
min_value=1e5,
|
|
||||||
)
|
|
||||||
self.add_setting(resonant_frequency_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
gamma_setting = FloatSetting(
|
|
||||||
self.GAMMA,
|
|
||||||
4.342e7,
|
|
||||||
"The gyromagnetic ratio of the sample’s nuclei.",
|
|
||||||
min_value=0,
|
|
||||||
)
|
|
||||||
self.add_setting(gamma_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
# This could be updated to a selection setting
|
|
||||||
nuclear_spin_setting = FloatSetting(
|
|
||||||
self.NUCLEAR_SPIN,
|
|
||||||
9 / 2,
|
|
||||||
"The nuclear spin of the sample’s nuclei.",
|
|
||||||
min_value=0,
|
|
||||||
)
|
|
||||||
self.add_setting(nuclear_spin_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
spin_factor_setting = FloatSetting(
|
|
||||||
self.SPIN_FACTOR,
|
|
||||||
2,
|
|
||||||
"The spin factor represents the scaling coefficient for observable nuclear spin transitions along the x-axis, derived from the Pauli I x 0 -matrix elements.",
|
|
||||||
min_value=0,
|
|
||||||
)
|
|
||||||
self.add_setting(spin_factor_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
powder_factor_setting = FloatSetting(
|
|
||||||
self.POWDER_FACTOR,
|
|
||||||
0.75,
|
|
||||||
"A factor representing the crystallinity of the solid sample. A value of 0.75 corresponds to a powder sample.",
|
|
||||||
min_value=0,
|
|
||||||
max_value=1,
|
|
||||||
)
|
|
||||||
self.add_setting(powder_factor_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
filling_factor_setting = FloatSetting(
|
|
||||||
self.FILLING_FACTOR,
|
|
||||||
0.7,
|
|
||||||
"The ratio of the sample volume that occupies the coil’s sensitive volume.",
|
|
||||||
min_value=0,
|
|
||||||
max_value=1,
|
|
||||||
)
|
|
||||||
self.add_setting(filling_factor_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
t1_setting = FloatSetting(
|
|
||||||
self.T1,
|
|
||||||
83.5e-5,
|
|
||||||
"The longitudinal or spin-lattice relaxation time of the sample, influencing signal recovery between pulses.",
|
|
||||||
min_value=1e-6,
|
|
||||||
)
|
|
||||||
self.add_setting(t1_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
t2_setting = FloatSetting(
|
|
||||||
self.T2,
|
|
||||||
396e-6,
|
|
||||||
"The transverse or spin-spin relaxation time, determining the rate at which spins dephase and the signal decays in the xy plane",
|
|
||||||
min_value=1e-6,
|
|
||||||
)
|
|
||||||
self.add_setting(t2_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
t2_star_setting = FloatSetting(
|
|
||||||
self.T2_STAR,
|
|
||||||
50e-6,
|
|
||||||
"The effective transverse relaxation time, incorporating effects of EFG inhomogeneities and other dephasing factors.",
|
|
||||||
min_value=1e-6,
|
|
||||||
)
|
|
||||||
self.add_setting(t2_star_setting, self.SAMPLE)
|
|
||||||
|
|
||||||
self.averages = 1
|
|
||||||
self.target_frequency = 100e6
|
|
||||||
|
|
||||||
@property
|
|
||||||
def averages(self):
|
|
||||||
"""The number of averages used for the simulation.
|
|
||||||
|
|
||||||
More averages improve the signal-to-noise ratio of the simulated signal.
|
|
||||||
"""
|
|
||||||
return self._averages
|
|
||||||
|
|
||||||
@averages.setter
|
|
||||||
def averages(self, value):
|
|
||||||
self._averages = value
|
|
||||||
|
|
||||||
@property
|
|
||||||
def target_frequency(self):
|
|
||||||
"""The target frequency for the simulation.
|
|
||||||
|
|
||||||
Doesn't do anything at the moment.
|
|
||||||
"""
|
|
||||||
return self._target_frequency
|
|
||||||
|
|
||||||
@target_frequency.setter
|
|
||||||
def target_frequency(self, value):
|
|
||||||
self._target_frequency = value
|
|
||||||
|
|
@ -1,78 +0,0 @@
|
||||||
import unittest
|
|
||||||
import logging
|
|
||||||
import matplotlib.pyplot as plt
|
|
||||||
from quackseq.pulsesequence import QuackSequence
|
|
||||||
from quackseq.event import Event
|
|
||||||
from quackseq.functions import RectFunction
|
|
||||||
from quackseq.spectrometer.simulator import Simulator
|
|
||||||
|
|
||||||
# logging.basicConfig(level=logging.DEBUG)
|
|
||||||
|
|
||||||
|
|
||||||
class TestQuackSequence(unittest.TestCase):
|
|
||||||
|
|
||||||
def test_event_creation(self):
|
|
||||||
seq = QuackSequence("test - event creation")
|
|
||||||
seq.add_pulse_event("tx", "10u", 1, 0, RectFunction())
|
|
||||||
seq.add_blank_event("blank", "3u")
|
|
||||||
seq.add_readout_event("rx", "100u")
|
|
||||||
seq.add_blank_event("TR", "1m")
|
|
||||||
|
|
||||||
json = seq.to_json()
|
|
||||||
print(json)
|
|
||||||
|
|
||||||
sim = Simulator()
|
|
||||||
sim.set_averages(100)
|
|
||||||
|
|
||||||
result = sim.run_sequence(seq)
|
|
||||||
self.assertIsNotNone(result)
|
|
||||||
self.assertTrue(hasattr(result, "tdx"))
|
|
||||||
self.assertTrue(hasattr(result, "tdy"))
|
|
||||||
self.assertGreater(len(result.tdx), 0)
|
|
||||||
self.assertGreater(len(result.tdy), 0)
|
|
||||||
|
|
||||||
# Plotting the result can be useful for visual inspection during development
|
|
||||||
plt.plot(result.tdx, abs(result.tdy))
|
|
||||||
plt.show()
|
|
||||||
|
|
||||||
def test_simulation_run_sequence(self):
|
|
||||||
seq = QuackSequence("test - simulation run sequence")
|
|
||||||
|
|
||||||
tx = Event("tx", "10u", seq)
|
|
||||||
seq.add_event(tx)
|
|
||||||
seq.set_tx_amplitude(tx, 1)
|
|
||||||
seq.set_tx_phase(tx, 0)
|
|
||||||
|
|
||||||
json = seq.to_json()
|
|
||||||
print(json)
|
|
||||||
|
|
||||||
rect = RectFunction()
|
|
||||||
seq.set_tx_shape(tx, rect)
|
|
||||||
|
|
||||||
blank = Event("blank", "3u", seq)
|
|
||||||
seq.add_event(blank)
|
|
||||||
|
|
||||||
rx = Event("rx", "100u", seq)
|
|
||||||
seq.set_rx(rx, True)
|
|
||||||
seq.add_event(rx)
|
|
||||||
|
|
||||||
TR = Event("TR", "1m", seq)
|
|
||||||
seq.add_event(TR)
|
|
||||||
|
|
||||||
sim = Simulator()
|
|
||||||
sim.set_averages(100)
|
|
||||||
|
|
||||||
result = sim.run_sequence(seq)
|
|
||||||
self.assertIsNotNone(result)
|
|
||||||
self.assertTrue(hasattr(result, "tdx"))
|
|
||||||
self.assertTrue(hasattr(result, "tdy"))
|
|
||||||
self.assertGreater(len(result.tdx), 0)
|
|
||||||
self.assertGreater(len(result.tdy), 0)
|
|
||||||
|
|
||||||
# Plotting the result can be useful for visual inspection during development
|
|
||||||
plt.plot(result.tdx, abs(result.tdy))
|
|
||||||
plt.show()
|
|
||||||
|
|
||||||
|
|
||||||
if __name__ == "__main__":
|
|
||||||
unittest.main()
|
|
||||||
Loading…
Reference in a new issue